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from mpi4py import MPI
from mpi4py.futures import MPICommExecutor
from openbabel import pybel
from Bio import SeqIO
import os
def parse_complex(fn):
try:
name = os.path.basename(fn).split('.')[0]
print(name)
seq = str(next(SeqIO.parse(fn, "pdb-seqres")).seq)
return name, seq
except:
return None
if __name__ == '__main__':
import glob
filenames = glob.glob('binding_moad/BindingMOAD_2020/*.bio1')
comm = MPI.COMM_WORLD
with MPICommExecutor(comm, root=0) as executor:
if executor is not None:
result = executor.map(parse_complex, filenames)
result = list(result)
names = [r[0] for r in result if r is not None]
seqs = [r[1] for r in result if r is not None]
import pandas as pd
df = pd.DataFrame({'name': names, 'seq': seqs})
df.to_parquet('data/moad_complex.parquet')
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